Controlling false discovery rates in factorial experiments with between-subjects and within-subjects tests

• Published in: BMC research notes Vol. 6; no. 1; p. 204
• Main Authors: Schoen, Eric D, Rubingh, Carina M, Wopereis, Suzan, van Erk, Marjan
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 21.05.2013; BioMed Central
• Subjects: Analysis; Analysis of Variance; Body mass index; Diet; Expected values; Factorial experiment designs; False Positive Reactions; Medical research; Medicine, Experimental; Methods; Studies; Technical Note; Variables; Netherlands
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/1756-0500-6-204

The False Discovery Rate (FDR) controls the expected number of false positives among the positive test results. It is not straightforward how to conduct a FDR controlling procedure in experiments with a factorial structure, while at the same time there are between-subjects and within-subjects factors. This is because there are P-values for different tests in one and the same response along with P-values for the same test and different responses. We propose a procedure resulting in a single P-value per response, calculated over the tests of all the factorial effects. FDR control can then be based on the set of single P-values. The proposed procedure is very easy to apply and is recommended for all designs with factors applied at different levels of the randomization, such as cross-over designs with added between-subjects factors. NCT00959790.